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Monthly Archives: September 2007

The senate will vote during the week beginning October 15 on a bill that changes the NIH Open Access deposit policy from a request (which has generated about 5% compliance) to a mandate. This would be a leap forward for OA and science, not only in the US but throughout the world. If you’re a US resident, please take a few minutes to write to your Senators in support of this bill. (Letters should arrive by close of business Oct 12.)
The American Library Association has made it trivially easy to contact your congresscritters about this: go to their action alert, fill in your zip code, write a brief letter and hit send. For help in composing a letter, see Peter Suber’s collection of talking points, background and other resources. Below is the letter I sent.

Dear Congresscritter,
I am a research scientist and (pending final approval) about to become a US citizen. I have worked in the US for four years, having held an NIH T32 postdoctoral fellowship for two of those years. As a scientist and as a concerned member of the US public, I am writing to urge you to approve without change that portion of the Senate Appropriations Committee’s FY 2008 Labor-HHS-Education appropriations bill which directs the NIH to change its policies from a request to a mandatory requirement for free, timely public access to NIH funded research.
The US, through the NIH, invests roughly $30 billion in medical research every year. While the return on this investment is significant, it is far lower than it should be — and mandatory Open Access is the answer.
Open Access maximizes research efficiency (and thus the return on research investment) by removing obstacles to the acquisition of new results by researchers (1), and is essential for realizing the vast and virtually untapped potential of automated data- and text-mining (2, 3). Traditional scientific publishing sees the taxpayer pay for the research, pay to have it published, and then pay again to access it (or for the same researchers to access it!) through subscriptions to privately owned journals (4). Legislators have a practical, legal and moral obligation to end this inefficiency and waste.
In the two years since its instigation, the current voluntary policy has resulted in less than 5% of NIH funded research being deposited in the National Library of Medicine’s public archive; a mandate is clearly necessary.
Finally, please do not be taken in by dishonest, self-interested arguments put forward by the traditional publishing lobby. Open Access is entirely compatible with all existing copyright schemes, will have no negative effect on peer review and does not involve any form of censorship or government interference in research or in publishing (5). Moreover, the NIH estimates (6) that implementation of the mandatory Open Access policy will cost less than 10% of the $30 million/year the NIH already pays directly to publishers in the form of page charges.
Open Access is necessary if US research is to flourish as it should, and mandatory deposit in the NLM or an equivalent archive is necessary to support Open Access to publicly funded research. Please approve without change that portion of the appropriations bill which changes the language of the NIH deposit policy from voluntary to mandatory.
Sincerely,
me.
—–references—–
(1) http://eprints.ecs.soton.ac.uk/10713/01/timcorr.htm
(2) http://eprints.ecs.soton.ac.uk/13028/01/AS-OA-final.pdf
(3) http://www.jneurosci.org/cgi/content/full/26/38/9606
(4) http://www.earlham.edu/%7Epeters/fos/newsletter/09-04-03.htm#taxpayer
(5) http://www.earlham.edu/~peters/fos/2007_08_19_fosblogarchive.html#365179758119288416
(6) http://grants.nih.gov/grants/guide/notice-files/NOT-OD-05-022.html

Well, one answer is that they are MEFs — mouse embryo fibroblasts — since that’s what I started with. Only the cells pictured are pretty clearly not regular fibroblasts; they look more like neurons or macrophages of some kind. MEFs are a mixed population, consisting of whatever grows out of a dissociated (minced) mouse embryo minus the head, so there are some early neural and immune cells in the mix. The cells pictured are what remains after selection with either G418 or puromycin — I was making stably transfected cells, and this is one of the control plates.
So what I’m wondering is, would a brief period of exposure to a selective agent like puro be a good way to isolate naturally resistant populations, and what would those populations contain? (Of course, whatever these things are, the most likely explanation for their resistance is terminal differentiation, so they’re simply dying more slowly — I haven’t tried taking away the selective agent to see whether they will multiply.)
Any ideas, lazyweb?

I’ve noticed that whenever I come all over jackass, it’s because there’s something wrong with my position — when I’m secure about something I seldom resort to snark. Outright venom, sure; snide formality and similar oily tricks, no.
Case in point: I took an uncalled-for swipe at Maxine (again because I hadn’t thought my ownposition through properly), and though I’ve apologized, I ought not be surprised or feel put-upon if people point to that incident as an example of bad online manners. But I feel bad about it, so mention of it gets me all defensive.
This is doubly daft, since not only is such a response self-evidently counterproductive, I have no particular fear of being wrong. I’m a scientist: it’s in my nature and my training to attach no value judgement to being right or wrong: what matters is to see as clearly as possible and make the best models we can. So being wrong in public holds no terrors for me; it’s being a jackass that is embarrassing, and — catch 22, or something! — I do that when I suspect I’m wrong.
Don’t most people figure this stuff out when they’re about 12? Oy.
On the silver lining side, catching myself tending to snottery would be a good early warning that I’m wrong or uncertain about something, if I did it before being a jackass. I remember reading somewhere that all satori have to be repeated before they take hold, so maybe writing them down will also help…

A case in point is the criticism that my NPG colleague, Maxine Clarke, faced when talking about “open access” projects at NPG. Not everyone shared her definition of open access and she was accused by somebloggers of using the term as a marketing slogan. (Peter Murray-Rust, who made the original point, later recanted when he understood that Maxine was being genuine, so I don’t take issue with him.)

Mr Hannay does, presumably, take issue with me. I will apply Hanlon’s Razor and assume Mr Hannay did not bother to read beyond the post he linked, since the very next is this one:

In the entry below, I was not sufficiently careful to avoid Nature-bashing, or the implication that Maxine Clarke was morphing, werewolf-like, into some kind of publisher pitbull. Thanks to Pedro, bdf and RPM for responses which made this clear.
[…]
Let me finish, though, by pointing out that I do not wish to paint NPG as one of the unscrupulous publishers whose intentions worry me, nor Maxine Clarke as their sneaky shill. If NPG uses the term “open access” differently from me, I take that as a good-faith disagreement, and if Maxine uses the term in her employers’ sense that is hardly “marketing”. Specifically, I apologize for the phrase “if [Maxine] is going to start abusing [the term “OA”] as marketing for Nature”, which contains an uncalled-for implication that I hope this entry will dispel.

The elision there includes the list of NPG’s OA-related activities that Mr Hannay goes on to point out. The next post on my blog is this one in which I quote Peters Suber and Murray-Rust some more regarding OA definitions and conclude, in what I am happy to have readers interpret as a further step back:

I take Peter S to be saying that it’s inevitable that “Open Access” will come to mean, in general use, more things to more people than strict BOAI, and we will not achieve anything by making arseholes of ourselves over it. (Even if that’s not quite the way Peter S would put it, that’s the way I’ve come to look at the situation.) There’s no point in picking quarrels we don’t have to have. It’s enough to be more careful in our own usage, for which purposes suffixes a la Peter MR should prove very useful when we need extra precision. I don’t think we need invent terms (“fuzzy”) just yet — “OA (specific licence, with hyperlink if writing online)” and “OA (free to read)” should cover most cases.
If we can get to the point where the average consumer — basically, any researcher — responds to an OA claim or label by asking “which licence?”, we will have done an end-run around the problem of term dilution.

It seems to me entirely unfair and misleading to link to the first of my posts without also linking the next two.
I think Mr Hannay is also in error in describing this post from Jean-Claude as a “followup” to the posts above; I think that Jean-Claude was referring to much more recent and clear-cut abuses outlined by Peter Murray-Rust.
Mr Hannay also goes on to say that

Some people are just too quick to assume base motives, and employ words like “boycott” as if they were punctuation marks.

I do not know who that is aimed at, but as for my own reference to a boycott, I do not think it unreasonable or precipitous to consider such action against publishers who do not distance themselves from PRISM and similar efforts. Why should it be up to me to determine who is and is not part of PRISM? The AAPThe PRISM organizers would certainly like me to assume that all their AAP members are PRISM supporters. As Mr Hannay himself makes clear, publishers need scientists more than the other way around. If you want my manuscripts, you had better demonstrate to me that you are not part of the pack of corporate bloodsuckers and soulless spin doctors that is pushing the palpably dishonest, profit-driven PRISM agenda. (Not that I would, given a free choice, publish in Nature anyway, even after Mr Hannay made it clear NPG does not support PRISM and even if they’d have me — because they’re not OA.)

Update: Peter Murray-Rust did a better job than me of responding to the Nascent post: he rightly led with the important part, which is that Nature is not endorsing PRISM. That’s no surprise, but I think it important to be explicit and public about who is and who is not backing PRISM.
Also, now I feel bad about the snotty “Mr Hannay” stuff. I use people’s first names here as a rule, even when I’ve never met them, because a blog is an informal conversation and because I think it fosters a sense of civil fucking discourse. I know perfectly well that Timo is on the side of the angels (viz, on the side of science!) when it comes to scientific communication, and it follows that his comments — and criticisms — on this issue are made in good faith. So, er, *shuffles feet*, sorry Timo.

Since I spend a fair bit of time excoriating publishers, it’s only fair that I take note of those who act in good faith. In response to the blogospheric reaction to the Nature mission statement, Maxine Clarke asked the appropriate persons to update the NPG web page (as you remember, Bob, the journal site already made clear the necessary distinction between the original and updated statements). Accordingly, the NPG page now reads:

and there follows the same version of the original that was on the page last time I looked.
It’s nitpicking to note that I prefer the way the journal does it, with the updated statement immediately visible and a link to the pdf of the original. The new page removes any confusion as to which mission statement now obtains.
Maxine also asked for the print edition of the journal to follow the online version and make both versions of the mission statement obvious. This will necessarily take more time than updating a web page, and I don’t have the latest Nature to hand so I don’t know if the print change has gone through yet. I will update again as soon as I find out.
So, many thanks to Maxine for responding to somewhat barbed criticism in such a constructive manner.

I’m swamped, but two quick points:
1. I’m not going to try to keep up with reactions to PRISM here, unless I think I have something potentially useful to add. If you want a news stream, read OAN or watch my PRISM tag on Simpy — I’ll grab everything I notice.
2. Peter Murray-Rust is blogging up a storm on publisher policies, copyright and Open Access:

There is a great deal of confusion regarding publisher policies and the rights of readers, scholars, institutions &c. I hope that publishers will agree with me that Peter MR is doing a sterling job of getting these issues out into the open, where they can be clarified — to everyone’s benefit.

I suspect that AAP/PSP did not consult its members before launching PRISM. But in any case the members should know that the launch of PRISM tarnishes them, alienates authors, readers, and referees, and, if successful, will only harm science by entrenching rather than removing access barriers to the results of publicly-funded research.

Peter is commenting there in response to someone else who has got the right idea, Peter Murray-Rust, who (as a Cambridge faculty member) has written to Cambridge University Press; his letter is an excellent example of what everyone should do who has any connection, professional or personal, with any of the AAP/PSP member companies, so I quote it here in full:

Open Letter to Stephen Bourne, Chief Executive Cambridge University Press
Dear Stephen Bourne,
I am writing as an individual member of staff in the University (heavily
engaged in developing new approaches to scientific scholarly publishing) to
ask about CUP’s involvement with the recently launched PRISM initiative
from the AAP (http://www.prismcoalition.org/). This initiative is an
undisguised coalition to discredit Open Access publishing and its launch a
few days ago has generated universal dismay and anger in many quarters
including several outside mainstream publishing. The press release was
reported in full by Peter Suber on his Open Access News blog
(http://feeds.feedburner.com/~r/earlham/dGCQ/~3/147374721/2007_08_19_fosblogarchive.html)
where he has objectively answered and dismissed the basis of PRISM and its
methods. As an example of the language of PRISM it implies that publishing
in Open Access journals (as I do on occasions) is “junk science”. There is
much more from PRISM which is both deliberately factually incorrect and
misleading and I cannot see how a reputable scholarly organisation such as
CUP could be associated with it. Indeed at least one similar publisher
(Rockefeller University Press
http://feeds.feedburner.com/~r/earlham/dGCQ/~3/150207794/2007_08_26_fosblogarchive.html)
writes:
“I am writing to request that a disclaimer be placed on the PRISM website
indicating that the views presented on the site do not necessarily reflect
those of all members of the AAP. We at the Rockefeller University Press
strongly disagree with the spin that has been placed on the issue of open
access by PRISM.” [rest of letter omitted here]
The purpose of my letter is simply to request factual information from CUP
about its involvement with PRISM. Since PRISM itself has not reacted to any
of the recent comment I can simply speculate that not all members of the
AAP (perhaps including yourselves) were consulted before PRISM made its
press release and new site. In particular it is unclear whether PRISM is de
facto composed of all the members of the AAP or whether it uses their
unsought goodwill to reinforce the apparent strength of the PRISM
organization.
This mail is an Open Letter (posted on my blog,
http://wwmm.ch.cam.ac.uk/blogs/murrayrust) and I would intend to publish
your reply in toto and unedited since your position (and those of similar
publishers) is of great public interest). If there is anything you would
not wish to be published, please indicate. Alternatively you may leave a
comment on the blog itself. (My blog itself, though strongly advocating
Open Access and particularly Open Data, attempts to be fair and accurate).
Thanks in advance
Peter Murray-Rust

This letter hits every necessary nail squarely on the head:

be polite

make clear the nature of your connection with the publisher to whom you are writing

explicitly request a specific response: did Publisher X know about PRISM, and does Publisher X support PRISM?

suggest that Publisher X should publicly distance themselves as RUP has done

if at all possible, do all of this in public: an open letter, on a blog

I don’t know whether I have any direct connection with any AAP/PSP member companies, although I could certainly write to publishers of journals in which I have published papers. In a later entry I will dig through the list and try to find likely recipients of such letters — for which Peter Murray-Rust has provided such a splendid template.Update: in comments on Jonathan’s post, CSHL Press has repudiated PRISM. Good for them, and I hope they will make a formal public statement to the same effect — for instance, on their website.